title: Mapping gene activity of Arabidopsis root hairs.
abstract: BACKGROUND
  Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized cells in the epidermis, represent an ideal model for cell fate acquisition and differentiation in plants.
  
  
  RESULTS
  Here, we provide an atlas of gene and protein expression in Arabidopsis root hair cells, generated by paired-end RNA sequencing and LC/MS-MS analysis of protoplasts from plants containing a pEXP7-GFP reporter construct. In total, transcripts of 23,034 genes were detected in root hairs. High-resolution proteome analysis led to the reliable identification of 2,447 proteins, 129 of which were differentially expressed between root hairs and non-root hair tissue. Dissection of pre-mRNA splicing patterns showed that all types of alternative splicing were cell type-dependent, and less complex in EXP7-expressing cells when compared to non-root hair cells. Intron retention was repressed in several transcripts functionally related to root hair morphogenesis, indicative of a cell type-specific control of gene expression by alternative splicing of pre-mRNA. Concordance between mRNA and protein expression was generally high, but in many cases mRNA expression was not predictive for protein abundance.
  
  
  CONCLUSIONS
  The integrated analysis shows that gene activity in root hairs is dictated by orchestrated, multilayered regulatory mechanisms that allow for a cell type-specific composition of functional components.
authors.forename: Ping
authors.initials: P
authors.lastname: Lan
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Li
authors.forename: Wen-Dar
authors.initials: WD
authors.lastname: Lin
authors.forename: Simonetta
authors.initials: S
authors.lastname: Santi
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schmidt
mesh_terms: D017398:Alternative Splicing; D017360:Arabidopsis / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D002454:Cell Differentiation; D005091:Exons; D018506:Gene Expression Regulation, Plant; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D007438:Introns; D058977:Molecular Sequence Annotation; D018517:Plant Roots / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D010957:Plasmids; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D011523:Protoplasts / Q000166:cytology / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; C472142:AtEXP7 protein, Arabidopsis; D020543:Proteome; D012333:RNA, Messenger; D018749:RNA, Plant; D049452:Green Fluorescent Proteins